I have a bikes direct bike and its great. I was unsure of it, but got in on Craig's list so I could try it out before buying. $400 for a bike that would have cost me $2000 at the bike store was nice. Makes a great commuter.

Components are generally similar, although you may want to upgrade the wheels. For general commuting it was great. I do find that for racing or high effort work, a branded bike will have the latest innovations and can be both more efficient and more comfortable to ride. Not a big deal when commuting though.

Biggest benefit from LBS: FIT. The biggest worry for me buying factory direct is making sure the bike fits and is comfortable. Any LBS will work on my bike, but if it doesn't fit, its just a waste of $$$. I recently bought a high end factory direct bike (canyon), and bought two sizes so I could ensure I dialed in the fit. Fortunately they have a good return policy - so while it was a hassle it worked. Much easier to go to the LBS, try out half a dozen (or more) bikes, and have the experts there ensure it fits you well.